Re: [maq-help] SNP filtering and calling
Status: Beta
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From: Heng Li <lh...@gm...> - 2007-11-28 09:36:53
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Dear Olivier, Thanks for the feed back. maq-0.6.2 and maq-0.6.1 use different rules in filtering SNPs. In maq-0.6.2, the following rules are used to get cns.final.snp: "After mapping and consensus base calling, we filtered the SNPs based on four rules: [i') discard SNPs in 3bp-flanking regions beside potential indels;] i) discard SNPs covered by three or fewer reads; ii) discard SNPs covered by no read with a mapping quality higher than 40; iii) in any 10bp window, if there are 3 or more SNPs, discard them all; and iv) discard SNPs with quality smaller than 40." In some cases, you can reduce the threshold on the quality of SNP (rule iv), but the false positive may increase a little. For single- end reads, you may also try: maq.pl SNPfilter -a cns.snp > cns.filtered.snp This command will invoke an alternative filter which is with similar aim but slightly different from rule ii). As for the last column in *.snp, you can ignore them. Even I do not use them any longer. Maybe I should remove that column some day. Hope this helps. Cheers, Heng On 27 Nov 2007, at 22:20, Olivier Harismendy wrote: > Hi, > > I have question about the cns.final.snp output file from maq.pl > easyrun. > > What are the filters applied to the SNPs (depth/repeats/quality) ? > Is there a way to play with the parameters ? > > In the output, the last column (quality difference between strong > and weak allele) doesn't make sense to me as the values go from > -124 to 124. Can you explain a little ? > > thanks for your answer. > > Olivier > > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > maq-help mailing list > maq...@li... > https://lists.sourceforge.net/lists/listinfo/maq-help |